Genezoom

GeneZoom plot is a visualization tool that shows the frequency of variants in a predefined region for groups of individuals. It takes an annotated VCF file as input and generate a text file with specific variant information extracted from VCF file. An R script is used to draw GeneZoom plot based on the text file.

Because all reference data are version hg19, please make sure that your VCF file is also version hg19.

Get geneZoom Source Codes

Download from webpage

Through this link geneZoom Download, you can download a copy of geneZoom.

Download from GitHub with Git

You can create your own git clone(copy) using:

 git clone https://github.com/jinchen-umich/geneZoom.git

or

 git clone git://github.com/jinchen-umich/geneZoom.git

Either of these two commands creates a directory called geneZoom in the current directory.

Update your copy

If you have already downloaded your copy, use the following commands to update:

 1. cd pathToYourCopy/geneZoom
 2. git pull

Download From GitHub without Git

If there is no git in your system, you can still download from GitHub:

1. Latest Code (master branch)

   via Website

   1. Go to : https://github.com/jinchen-umich/geneZoom
   2. Click on the Download ZIP button on the right side panel.

   via Command Line

   wget https://github.com/jinchen-umich/geneZoom/archive/master.zip

After downloading the file, uncompress (unzip/untar) it. The directory created will be named geneZoom.

Build geneZoom

To build geneZoom, copy the geneZoom package to the directory you want, and then run the following command:

 tar xzvf geneZoom.tar.gz

After you unzip, you can find 3 directories in "geneZoom" (./example ./lib ./scripts ./ref).

Basic Usage Example

When you run

 perl geneZoom.pl

you will get some information about geneZoom

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GeneZoom.pl :

---

This tool is a visualization tool that shows the frequency of variants in a predefined region for groups of individuals.

Note: The SNPs and VCF should be hg19 version. VCF file must have the header greater than 4.0 version. This tool will run ANOVAR to annotate VCF. The annotation values should be in the value list of ANOVAR(http://www.openbioinformatics.org/annovar/annovar_gene.html).

Version : 1.0.1

Report Bug(s) : jich[at]umich[dot]edu

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Usage : perl GeneZoom.pl --vcf vcf --phenotypeFile phenotypeFile --sampleFieldName sample --phenotypeFieldName phenotype --phenotypeDelim tab/comma/blank --snpList snpList --flag "splicing:0.01:0.02,nonsense:blue,missense" --format pdf --outDIR outDIR

perl GeneZoom.pl --vcf vcf --phenotypeFile phenotypeFile --sampleFieldName sample --phenotypeFieldName phenotype --phenotypeDelim tab/comma/blank --snpList snpList --snpChrFieldName chr --snpPosFieldName pos --snpDelim tab/comma/blank --flag "splicing:green,nonsense:0.02:0.03,missense" --lables "chr1:123,chr2:234" --outDIR outDIR

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Get Help

When you run

 perl geneZoom.pl --man
 perl geneZoom.pl --help
 perldoc geneZoom.pl

You can get the help document.